Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1188

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 2419
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.41


Found at i:478 original size:21 final size:21

Alignment explanation


    Indices: 452--492  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        442 AGAATTTCCC

                                  
        452 TGTCCGGGTCAG-TTGTTTTAG
          1 TGTCCGGGTCAGATT-TTTTAG

                   *            
        473 TGTCCGGTTCAGATTTTTTA
          1 TGTCCGGGTCAGATTTTTTA

        493 TGCTTCTGGA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  21   16  0.89
  22    2  0.11

ACGTcount: A:0.12, C:0.15, G:0.27, T:0.46


Consensus pattern (21 bp):   
TGTCCGGGTCAGATTTTTTAG

Found at i:583 original size:15 final size:15

Alignment explanation


    Indices: 565--604  Score: 80
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        555 TCCCGGGTGG

                           
        565 GGGATATCCCAAAAA
          1 GGGATATCCCAAAAA

                           
        580 GGGATATCCCAAAAA
          1 GGGATATCCCAAAAA

                      
        595 GGGATATCCC
          1 GGGATATCCC

        605 GGTCCGGGTA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   25  1.00

ACGTcount: A:0.40, C:0.23, G:0.23, T:0.15


Consensus pattern (15 bp):   
GGGATATCCCAAAAA

Found at i:2307 original size:22 final size:21

Alignment explanation


    Indices: 2285--2363  Score: 70
    Period size: 22  Copynumber: 3.6  Consensus size: 21

       2275 TGGGGTTTTG

                    *            *
       2285 GGGTTATATGGTTTTGAGATTG
          1 GGGTT-TAGGGTTTTGAGATTA

                            *      
       2307 GGGTTT-GGGTTTTAGGGATTTA
          1 GGGTTTAGGGTTTT-GAGA-TTA

                              *   
       2329 GGGTTTTAGGGTTTTGAGTTTA
          1 GGG-TTTAGGGTTTTGAGATTA

                   *     
       2351 GGGTTTATGGTTT
          1 GGGTTTAGGGTTT

       2364 GGAGTTTTGG


Statistics
Matches: 47,  Mismatches: 6, Indels: 9
        0.76            0.10        0.15

Matches are distributed among these distances:
  20    6  0.13
  21   13  0.28
  22   16  0.34
  23    5  0.11
  24    7  0.15

ACGTcount: A:0.14, C:0.00, G:0.38, T:0.48


Consensus pattern (21 bp):   
GGGTTTAGGGTTTTGAGATTA

Found at i:2333 original size:44 final size:44

Alignment explanation


    Indices: 2262--2356  Score: 109
    Period size: 44  Copynumber: 2.2  Consensus size: 44

       2252 TTTGGGGTGG

                *         *   *   *        *            
       2262 GGGGATTGGGGTTTGGGGTTTTGGGGTTATATGGTTTTGAGATT
          1 GGGGTTTGGGGTTTAGGGATTTAGGGTTATAGGGTTTTGAGATT

                      *                 *            *  
       2306 GGGGTTTGGGTTTTAGGGATTTAGGGTTTTAGGGTTTTGAGTTT
          1 GGGGTTTGGGGTTTAGGGATTTAGGGTTATAGGGTTTTGAGATT

            *      
       2350 AGGGTTT
          1 GGGGTTT

       2357 ATGGTTTGGA


Statistics
Matches: 42,  Mismatches: 9, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  44   42  1.00

ACGTcount: A:0.12, C:0.00, G:0.43, T:0.45


Consensus pattern (44 bp):   
GGGGTTTGGGGTTTAGGGATTTAGGGTTATAGGGTTTTGAGATT

Found at i:2416 original size:14 final size:14

Alignment explanation


    Indices: 2304--2418  Score: 65
    Period size: 14  Copynumber: 8.1  Consensus size: 14

       2294 GGTTTTGAGA

                 *        
       2304 TTGGGGTTTGGGTT
          1 TTGGGTTTTGGGTT

                      *     
       2318 TTAGGGATTTAGGGTT
          1 TT-GGG-TTTTGGGTT

                       *   
       2334 TTAGGGTTTTGAGTT
          1 TT-GGGTTTTGGGTT

             *             
       2349 TAGGGTTTAT-GG-T
          1 TTGGGTTT-TGGGTT

                           
       2362 TTGGAGTTTT-GGTT
          1 TTGG-GTTTTGGGTT

                  * ** *  
       2376 TTGGGTGTAAGATT
          1 TTGGGTTTTGGGTT

             *    * *     
       2390 TGGGGTATCGGGTT
          1 TTGGGTTTTGGGTT

                          
       2404 TTGGGTTTTGGGTT
          1 TTGGGTTTTGGGTT

             
       2418 T
          1 T

       2419 A


Statistics
Matches: 77,  Mismatches: 18, Indels: 12
        0.72            0.17        0.11

Matches are distributed among these distances:
  13   10  0.13
  14   42  0.55
  15   12  0.16
  16   13  0.17

ACGTcount: A:0.10, C:0.01, G:0.40, T:0.49


Consensus pattern (14 bp):   
TTGGGTTTTGGGTT
Done.